Shopify payments setup after WooCommerce (2026)

Payment gateway setup is one of the first things to configure after migrating to Shopify — your store cannot take real orders until payments are live. WooCommerce payment setup involved installing individual gateway plugins (WooCommerce Stripe, WooCommerce PayPal Payments, WooCommerce Klarna), each with its own configuration. Shopify consolidates this through a single Payments settings page, with Shopify Payments as the native option and a clean interface for adding third-party gateways. This guide covers the full payment setup post-migration.

Payment gateway comparison: WooCommerce vs Shopify

WooCommerce	Shopify equivalent	Notes
WooCommerce Stripe plugin	Shopify Payments (powered by Stripe) or Stripe via third-party	Shopify Payments preferred — no extra transaction fee
WooCommerce PayPal Payments plugin	PayPal (via Shopify Payments or standalone)	PayPal available as express checkout option
WooCommerce Klarna plugin	Klarna via Shopify Payments (UK/EU) or third-party	BNPL included in Shopify Payments where available
WooCommerce Clearpay plugin	Clearpay via Shopify Payments (UK)	Included in Shopify Payments UK
Stripe direct integration	Shopify Payments (Stripe-based) or Stripe as third-party gateway	Third-party Stripe: 0.5–2% extra transaction fee
SagePay / Opayo	Opayo third-party gateway on Shopify	Available as a third-party gateway — transaction fee applies
WorldPay	WorldPay third-party gateway	Available on Shopify — transaction fee applies

Shopify Payments: the native option

Shopify Payments is the recommended first choice for UK and US stores:

• No transaction fee: Using Shopify Payments avoids the Shopify transaction fee (0.5%–2% depending on plan). Using any third-party gateway incurs this fee on top of gateway fees.
• Powered by Stripe: Same Stripe infrastructure — same card acceptance rates, same security standards, same fraud tools.
• Included payment methods: Shopify Payments includes: all major credit/debit cards, Apple Pay, Google Pay, Shop Pay. In the UK: Klarna and Clearpay are available as BNPL options within Shopify Payments.
• Activation: Settings → Payments → Shopify Payments → Complete account setup. Requires: business legal name, registered address, director/owner details, bank account for payouts.
• Payout schedule: UK payouts typically 2–3 business days. US payouts next business day after $25+ balance.
• Availability: Shopify Payments is available in: US, UK, Canada, Australia, Ireland, France, Germany, Spain, Italy, Netherlands, and others. Not available everywhere — check the Shopify help centre for your country.
• Prohibited products: Shopify Payments has a list of prohibited and restricted products (similar to Stripe). Review before activating if selling CBD, age-restricted items, digital goods with high chargeback risk, etc.

Third-party payment gateways

If Shopify Payments isn't available in your country, or if you need a specific gateway (e.g., Opayo for existing contracts, PayPal exclusively), configure a third-party gateway:

• Settings → Payments → Payment providers → Choose third-party provider
• Supported gateways: 100+ gateways including Stripe, PayPal, Braintree, Opayo, WorldPay, Adyen, Mollie, 2Checkout, and many regional providers
• Transaction fee: every third-party gateway incurs Shopify's transaction fee on top of the gateway's own fees: 2% (Basic), 1% (Shopify), 0.5% (Advanced), 0% (Plus)
• Exception: Shopify Payments third-party provider option allows some providers to be connected without the transaction fee — check if your gateway is listed under the no-fee option

PayPal setup

• PayPal is available as an express payment button alongside your main gateway (not as a replacement)
• Shopify Payments stores: add PayPal as a separate wallet option in Settings → Payments → Wallets and accelerated checkouts → PayPal Express Checkout
• PayPal business account: required. Connect your existing PayPal business account to Shopify.
• PayPal Express at checkout: shown as a button alongside Shop Pay, Apple Pay, and Google Pay in the express checkout section. Customers can pay in 2 clicks without entering card details.
• PayPal transaction fees: separate from Shopify Payments. PayPal charges their own fee (1.2%–2.9% + 30p in UK) on top of Shopify's transaction fee if not using Shopify Payments as primary.

Buy Now Pay Later (BNPL)

BNPL options significantly increase average order value, particularly for higher-ticket items (£100+):

• Klarna: Available in UK/EU via Shopify Payments. Offers "Pay in 3" (interest-free) and "Pay in 30 days". Merchant pays a fee per transaction; customer pays nothing unless they miss a payment.
• Clearpay (Afterpay): Available in UK via Shopify Payments. "Pay in 4" — 4 interest-free instalments over 6 weeks.
• Laybuy: 6 weekly interest-free payments — available for some Shopify markets via third-party gateway.
• Shop Pay Instalments: Available in US. 4 interest-free payments powered by Affirm. Within Shopify Payments.
• WooCommerce BNPL migration: WooCommerce Klarna and Clearpay plugins stored no customer data on your server — cancellation of the plugin and setup in Shopify is clean. Existing payment plans in progress at migration time must be honoured by the original gateway; new orders post-migration go through Shopify.

Apple Pay and Google Pay

• Apple Pay: automatically enabled when using Shopify Payments. Requires your store to be served over HTTPS (Shopify handles this). Apple Pay button appears on product pages and checkout for eligible Safari/iOS users.
• Google Pay: automatically enabled with Shopify Payments on Android Chrome users.
• Testing Apple Pay: use Safari on an iPhone with a card added to Apple Wallet. The Apple Pay button appears if you're on a real device — Apple Pay does not work in iOS Simulator.
• Dynamic checkout buttons: Shopify shows Apple Pay, Google Pay, and Shop Pay buttons on product pages (above the "Add to Cart" button). Enable in Settings → Payments → Accelerated checkouts.

Multi-currency payments

• Shopify Payments multi-currency: customers can browse and checkout in their local currency. Exchange rates updated daily. Enable in Settings → Payments → Currencies.
• UK stores: enable GBP (primary) + EUR (for Irish/EU customers) + USD (for US traffic)
• Payouts: all payouts convert to your home currency. Shopify uses Shopify's published exchange rate (with a small conversion fee).
• Shopify Markets: multi-currency is tied to Shopify Markets — each market can have its own currency, language, and pricing. Set up markets first (Settings → Markets), then currency per market.
• Manual exchange rates: Shopify Payments sets exchange rates automatically. For specific pricing (e.g., £100 in UK, €110 in EU — not just the converted rate), use Shopify Markets price adjustments.

Fraud prevention

• Shopify Payments fraud analysis: built-in fraud scoring on every order. Shopify highlights orders with risk indicators (address mismatch, high-risk country, proxy IP). Review high-risk orders before fulfilling.
• 3D Secure (3DS): Shopify Payments supports 3DS2 for European SCA (Strong Customer Authentication) requirements. No configuration needed — Shopify handles SCA compliance automatically.
• AVS and CVV checks: enabled by default in Shopify Payments. Decline orders that fail AVS or CVV checks if your risk tolerance is low.
• Chargebacks: Shopify Payments provides chargeback management in admin. Respond to chargebacks directly in the Shopify admin with evidence.

Payment setup checklist

• Activate Shopify Payments — complete business verification (legal name, address, director details, bank account)
• Confirm payout schedule and bank account details
• Enable PayPal Express as additional wallet option
• Enable Klarna and/or Clearpay via Shopify Payments (UK)
• Enable Apple Pay and Google Pay accelerated checkout buttons
• Configure multi-currency if selling internationally
• Review Shopify Payments prohibited products list — confirm products comply
• Test checkout with a real card (or test mode) — verify card payment, Apple Pay, and PayPal all work
• Verify 3DS challenge appears for SCA-required transactions (EU cards)
• Set up fraud risk thresholds in Shopify Payments settings
• Cancel WooCommerce payment gateway subscriptions (Stripe fee plugins, PayPal plugin, Klarna plugin) post-migration

The transaction fee calculation is the most financially significant payment decision when migrating to Shopify. A store processing £50,000 per month in orders that uses Stripe as a third-party gateway (instead of Shopify Payments) on the Basic Shopify plan pays an additional 2% transaction fee — £1,000 per month, £12,000 per year. That additional cost alone covers the price difference between Basic and Advanced Shopify plans, which reduces the transaction fee to 0.5%. Calculate your monthly order volume, apply the transaction fee for your plan, and determine whether a plan upgrade pays for itself. In most cases, stores above £20,000 per month should be on Advanced Shopify purely for the reduced transaction fee — the maths are straightforward.